International Conference Papers

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Subject: search.filters.subject.de Bruijn Graphs

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    Fully Dynamic de Bruijn Graphs
    (Springer International Publishing, 2016-09-21) Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco
    We present a space- and time-efficient fully dynamic implementation of de Bruijn graphs, which can also support fixed-length jumbled pattern matching.
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    Bidirectional Variable-Order de Bruijn Graphs
    (Springer International Publishing, 2016-03-22) Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
    Implementing de Bruijn graphs compactly is an important problem because of their role in genome assembly. There are currently two main approaches, one using Bloom filters and the other using a kind of Burrows-Wheeler Transform on the edge labels of the graph. The second representation is more elegant and can even handle many graph-orders at once, but it does not cleanly support traversing edges backwards or inserting new nodes or edges. In this paper we resolve the first of these issues and partially address the second.